Quartet Sampling is a method to analyze molecular phylogenies by calculating branch support using repeated sampling of quartets. Quartet Sampling differs from other support methods by combining a set of of tests into a single, efficient framework to address phylogenetic discordance. QS is particularly useful for very large and data-sparse alignments or large phylogenomic datasets.
Version 1.3.1 - Adds RESULTS.node.count.csv that provides counts and representative topologies for the three quartet arragements. This is useful when QD is low in determining the more common discordant option.
For complete details, see the manual for Quartet Sampling (https://github.com/FePhyFoFum/quartetsampling/blob/master/quartetsampling.pdf).
Shuiyin Liu has created a new R-script that can visualize QS results:
https://github.com/ShuiyinLIU/QS_visualization
Please reference his URL separately, if you use this visualization script.
James B Pease, Joseph W Brown, Joseph F Walker, Cody E Hinchliff, Stephen A Smith. 2018. Quartet Sampling distinguishes lack of support from conflicting support in the green plant tree of life. American Journal of Botany. 105(3): 385–403. doi:10.1002/ajb2.1016
Link to publication: http://dx.doi.org/10.1002/ajb2.1016
Please also include the URL (https://www.github.com/fephyfofum/quartetsampling).
Be sure also to cite RAxML-ng, RAxML, PAUP, or IQ-TREE (depending on which engine you use).
- James B. Pease - www.peaselab.org
- Stephen A. Smith blackrim.org
- Cody Hinchliff
- Joseph W. Brown
- Joseph F. Walker
This file is part of 'quartetsampling'
'quartetsampling' is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
'quartetsampling' is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with Foobar. If not, see (http://www.gnu.org/licenses/).